1. Hl7 and the Clinical Genomics Work Group
Mukesh Sharma
Washington University in St. Louis

2. Agenda HL7 introduction Reference Information Model
Clinical Genomics Work Group
Clinical Genomics Work Group Accomplishments
Gene Expression DAM
Upcoming Activities
Useful Links

3. Health Level 7
HL7 was founded in 1987 and accredited in 1994 by the American National Standards Institute (ANSI).
Health Level Seven (HL7), is an all-volunteer, not-for-profit organization involved in development of international healthcare standards.
HL7 is also used to refer to some of the specific standards created by the organization (e.g., HL7 v2.x, v3.0, HL7 RIM) standards
Source:

4. What does the name mean?
Health Level 7 symbolizes the seventh layer of the International Standards Organization (ISO) Communications Model:
1. Physical: Connects the entity to the transmission media
2. Data Link: Provides error control between adjacent nodes
3. Network: Routes the information in the network
4. Transport: Provides end-to-end communication control
5. Session: Handles problems that are not communication issues
6. Presentation: Converts the information
7. Application: Provides different services to the applications
Source:

5. Health Level 7
HL7 and its members provide a framework (and related standards) for the exchange, integration, sharing, and retrieval of electronic health information.
v2.x of the standards, which support clinical practice and the management, delivery, and evaluation of health services, are the most commonly used in the world
Work Group Meetings/Balloting Cycles
3 times annually
January, May, September
>700 members attend the meetings.
Source:

6. Health Level 7
HL7 is one of several American National Standards Institute (ANSI) -accredited Standards Developing Organizations (SDOs) operating in the healthcare arena.
HL7 has been adopted by several national SDOs outside the U.S.
36 countries
These SDOs are not accredited by ANSI.
ISO adopted HL7 as a centre of gravity in international standardization and accredited HL7 as a partnering organization for mutual issuing of standards.
The first mutually published standard was ISO/HL :2006 Health informatics—HL7 version 3—Reference information model—Release 1
Source:

7. What is the Reference Information Model (RIM)?
The Reference Information Model (RIM) is the cornerstone of the HL7 Version 3 development process.
It is a shared model between all the domains (clinical data) from which all domains create their messages.
The RIM and the vocabulary domains are the bases for the semantic specification of message elements.
Current version 2.3.1
Available at
Graphics in folder rim0231g

8. Infrastructure (communications)
RIM v2.3.1
Entities
Roles
Acts
Infrastructure (communications)
Partic-ipation
graphics in package rim0231g

9. The HL7 Clinical Genomics (CG) Work Group
Established as a SIG in 2003
Mission To enable the standard use of patient-related genetic data such as DNA sequence variations and gene expression levels, for healthcare purposes (‘personalized medicine’) as well as for clinical trials & research
Work Products and Contributions to HL7 Processes The Work Group will collect, review, develop and document clinical genomics use cases in order to determine what data needs to be exchanged. The WG will review existing genomics standards formats such as BSML (Bioinformatics Sequence Markup Language), MAGE-ML (Microarray and Gene Expression Markup Language), LSID (Life Science Identifier) and other. This group will recommend enhancements to and/or extensions of HL7's normative standards for exchange of information about clinical genomic orders and observations. In addition, Clinical Genomics will seek to assure that related or supportive standards produced by other HL7 groups are robust enough to accommodate their use in both research and clinical care use. The group will also monitor information interchange standards developed outside HL7, and attempt harmonization of information content and representation of such standards with the HL7 content and representation.

10. CG Work Group Leadership (Co-Chairs)
Joyce Hernandez
Merck & Co. Inc.
Kevin Hughes MD   Partners HealthCare System, Inc.
Amnon Shabo, PhD
IBM
Mollie Ullman-Cullere   Partners HealthCare System, Inc.

11. Formal Relationships with Other HL7 Groups
CG Work Group coordinates with a large number of other Work Groups in order to accomplish its mission. Strongest relationships are with
Orders and Observation
Clinical Statement
Clinical Decision Support
Regulated Clinical Research Information Management
Patient Care
Electronic Health Records
Modeling and Methodology
Structured Documents

12. Accomplishments Focus on V2 and V3 genetic and genomics data models
V3 Genetic Models
Single Gene (Genetic Locus) Common Message Elements (CMET)
Draft Standard for Trial Use – May 2005 (Revised May 2006)
Multiple Gene (Genetic Loci) CMET
Draft Standard for Trial Use – Jan 2007
Unified Full Genetic Variation CMET
Draft Standard for Trial Use – Jan 2008
Normative – Jan 2010
V3 Pedigree Topic - Family History
Normative – May, 2007

13. Accomplishments Genetic Variation V2 message
Developed for clinical practice to carry findings from a lab to a physician, genetic councilor, etc.
Subset of full V3 model, focus on interpretive, not raw (sequence) data
Genetic Variation V3 Reduced CMET
Companion to V2 message
Gene Expression Model
Intended for V2 and V3 implementation
Domain Analysis Model balloted Sept 2009, currently in Ballot May 2010

14. CG Gene Expression Domain Analysis Model-Diagram

15. CG Gene Expression Domain Analysis Model-Details
Subpackages
Array Design
Classes e.g Array, ArrayDesign, ArrayGroup, Reporter etc.
Common Classes
Identifiable, OntologySource, OntologyTerm etc.
Data
DataFile, DataMatrix, Image, ImageAcquistion etc.
Design Element
DesignElement, DimensionElement etc.
Experiement Definition
GenomicProtocol, LabExperiment, NormalizationTypes, ProtocolParameter etc.
Relationship
Relationships between: Samples, Arrays and Data
Bio-Specimen Diagrams
Classes e.g BioSpecimen, Bio-Specimen-Characteristics, Specimen Handling etc.

16. Clinical Genomics Domain Analysis Model-Terminology
Terminology: definitions from NCI EVS team for a number of terms needed for genetic sample type entries
nDNA (Nuclear DNA)
pDNA (plasmid DNA)
RNA (Ribonucleic acid)
RNAP (RNA polymerase)
mRNA (Messenger Ribonucleic Acid)
snRNA (Small nuclear RNA)
miRNA (microRNA)
ssRNA (single-stranded RNA)
dsRNA (double-stranded RNA)
snoRNA (small nucleolar RNA)
tRNA (Transfer RNA)
hnRNA (heterogeneous nuclear RNA)
RNP (Ribonucleoprotein)
snRNP (small nuclear ribonucleoproteins)

17. CG Gene Expression Domain Analysis Model-Ballot
Model available at
Comments due May 9, 2010
Under review by IRWG (ICR WS)
Model will be expanded in future to include Genetic Variations

18. Upcoming Activities Cytogenetic Lab Results
Project Scope statement being prepared
Model would consider classes from caBIO
Gene Expression Domain Analysis Model
Ballot reconciliation

19. Useful links HL7.org http://www.hl7.org/ HL 7 Wiki
Clinical Genomics Wiki
HL7 Standards
HL7v3 Ballot Site

20. Questions?

21. Additional slides

22. What does the name mean?
Health Level 7 symbolizes the seventh layer of the International Standards Organization (ISO) Communications Model:
1. Physical: Connects the entity to the transmission media
2. Data Link: Provides error control between adjacent nodes
3. Network: Routes the information in the network
4. Transport: Provides end-to-end communication control
5. Session: Handles problems that are not communication issues
6. Presentation: Converts the information
7. Application: Provides different services to the applications
HL7 isn't just Level 7 any more! After years of implementing HL7 v2.x, HL7 standard developers realized it was virtually impossible to develop a comprehensive standard without including other levels of the International Organization for Standardization (ISO) Open Systems Interconnect (OSI) Model. Today, work groups exist for XML, Security, Modeling & Methodology, Arden Syntax, CCOW and Vocabulary (

23. HL7 v3.0
HL7 V3, like V2.x, is a standard for exchanging messages among information systems that implement healthcare applications. However, V3 strives to improve the V2 process and its outcomes. The original process for defining HL7 messages was established in 1987 and has served well. The development principles behind HL7 V3 lead to a more robust, fully specified standard.
New capabilities offered in Version 3 include:
Top-down message development emphasizing reuse across multiple contexts and semantic interoperability
Representation of complex relationships
Formalisms for vocabulary support
Support for large scale integration
Solving re-use and interoperability across multiple domain contexts
A uniform set of models
Expanded scope to include community medicine, epidemiology, veterinary medicine, clinical genomics, security, etc.
From 1997

24. HL7 Development Framework: HDF
The basis for the specification of a messaging standard is a Reference Information Model (RIM) that completely covers the domain being addressed. The RIM and the vocabulary domains are the bases for the semantic specification of message elements. The Domain Information Model (DIM ) defines the information content for a specific area of expertise or interest. The DIM represents one group’s view of the world.
A proper subset of the RIM, called Refined Message Information Model (R-MIM) is used to express the information content for one or more related messages. The R-MIM provides one method of controlling optionality.
The Hierarchical Message Description (HMD) specifies a set of messages based of one R-MIM. A message type is specified in one HMD.
Source: